Source code for utils.box_residues

#!/usr/bin/env python3

"""Module containing the BoxResidues class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import  settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_vs.utils.common import *


[docs]class BoxResidues(BiobbObject): """ | biobb_vs BoxResidues | This class sets the center and the size of a rectangular parallelepiped box around a set of residues. | Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB. The residue identifiers that compose the selection (i.e. binding site) are provided by a property list. Args: input_pdb_path (str): PDB protein structure for which the box will be build. Its size and center will be set around the 'resid_list' property once mapped against this PDB. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476). output_pdb_path (str): PDB including the annotation of the box center and size as REMARKs. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box_residues.pdb>`_. Accepted formats: pdb (edam:format_1476). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **resid_list** (*list*) - (None) List with all the residue numbers to form a cavity or binding site. Mandatory property. * **offset** (*float*) - (2.0) [0.1~1000|0.1] Extra distance (Angstroms) between the last residue atom and the box boundary. * **box_coordinates** (*bool*) - (False) Add box coordinates as 8 ATOM records. * **residue_offset** (*int*) - (0) [0~1000|1] Residue id offset. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. Examples: This is a use example of how to use the building block from Python:: from biobb_vs.utils.box_residues import box_residues prop = { 'resid_list': [718, 743, 745, 762, 766, 796, 790, 791, 793, 794, 788], 'offset': 2, 'box_coordinates': True } box_residues(input_pdb_path='/path/to/myStructure.pdb', output_pdb_path='/path/to/newBox.pdb', properties=prop) Info: * wrapped_software: * name: In house using Biopython * version: >=1.76 * license: Apache-2.0 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_pdb_path, output_pdb_path, properties=None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) # Input/Output files self.io_dict = { "in": { "input_pdb_path": input_pdb_path }, "out": { "output_pdb_path": output_pdb_path } } # Properties specific for BB self.resid_list = properties.get('resid_list', []) self.offset = float(properties.get('offset', 2.0)) self.box_coordinates = float(properties.get('box_coordinates', False)) self.residue_offset = properties.get('residue_offset', 0) self.properties = properties # Check the properties self.check_properties(properties)
[docs] def check_data_params(self, out_log, err_log): """ Checks all the input/output paths and parameters """ self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"],"input_pdb_path", self.out_log, self.__class__.__name__) self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"],"output_pdb_path", False, self.out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` utils.box_residues.BoxResidues object.""" # check input/output paths and parameters self.check_data_params(self.out_log, self.err_log) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Parse structure fu.log('Loading input PDB structure %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log) structure_name = PurePath(self.io_dict["in"]["input_pdb_path"]).name parser = Bio.PDB.PDBParser(QUIET = True) structPDB = parser.get_structure(structure_name, self.io_dict["in"]["input_pdb_path"]) if len(structPDB): structPDB = structPDB[0] ## Mapping residue structure into input structure fu.log('Mapping residue structure into input structure', self.out_log, self.global_log) # Listing residues to be selected from the residue structure residPDB_res_list = [] for residPDB_res in self.resid_list: if self.residue_offset: residPDB_res_list.append((' ', residPDB_res+self.residue_offset, ' ')) else: residPDB_res_list.append((' ', residPDB_res, ' ')) selection_res_list = [] selection_atoms_num = 0 for struct_chain in structPDB: for struct_res in struct_chain: if struct_res.get_id() in residPDB_res_list: selection_res_list.append(struct_res) selection_atoms_num += len(struct_res.get_list()) if len(selection_res_list) == 0: fu.log(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"]), self.out_log) raise SystemExit(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"])) elif len(selection_res_list) != len(residPDB_res_list): fu.log('Cannot match all the residues listed in %s into %s. Found %s out of %s' % (', '.join(str(v) for v in self.resid_list),self.io_dict["in"]["input_pdb_path"], len(selection_res_list),len(residPDB_res_list)), self.out_log) else: fu.log('Selection of residues successfully matched', self.out_log, self.global_log) ## Compute binding site box size # compute box center selection_box_center = sum(atom.coord for res in selection_res_list for atom in res.get_atoms()) / selection_atoms_num fu.log('Binding site center (Angstroms): %10.3f%10.3f%10.3f' % (selection_box_center[0],selection_box_center[1],selection_box_center[2]), self.out_log, self.global_log) # compute box size selection_coords_max = np.amax([atom.coord for res in selection_res_list for atom in res.get_atoms()],axis=0) selection_box_size = selection_coords_max - selection_box_center if self.offset: selection_box_size = [c + self.offset for c in selection_box_size] fu.log('Binding site size (Angstroms): %10.3f%10.3f%10.3f' % (selection_box_size[0],selection_box_size[1],selection_box_size[2]), self.out_log, self.global_log) # compute volume vol = np.prod(selection_box_size) * 2**3 fu.log('Volume (cubic Angstroms): %.0f' % (vol), self.out_log, self.global_log) # add box details as PDB remarks remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (selection_box_center[0],selection_box_center[1],selection_box_center[2]) remarks += " SIZE:%10.3f%10.3f%10.3f" % (selection_box_size[0],selection_box_size[1],selection_box_size[2]) selection_box_coords_txt = "" # add (optional) box coordinates as 8 ATOM records if self.box_coordinates: fu.log('Adding box coordinates', self.out_log, self.global_log) selection_box_coords_txt = get_box_coordinates(selection_box_center,selection_box_size) with open(self.io_dict["out"]["output_pdb_path"], 'w') as f: f.seek(0, 0) f.write(remarks.rstrip('\r\n') + '\n' + selection_box_coords_txt) fu.log('Saving output PDB file (with box setting annotations): %s' % (self.io_dict["out"]["output_pdb_path"]), self.out_log, self.global_log) return 0
[docs]def box_residues(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` class and execute the :meth:`launch() <utils.box_residues.BoxResidues.launch>` method.""" return BoxResidues(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path, properties=properties, **kwargs).launch()
[docs]def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_pdb_path', required=True, help='PDB protein structure for which the box will be build. Its size and center will be set around the \'resid_list\' property once mapped against this PDB. Accepted formats: pdb.') required_args.add_argument('--output_pdb_path', required=True, help='PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block box_residues(input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path, properties=properties)
if __name__ == '__main__': main()